Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Jaclyn M. Noshay, Alexandre P. Marand, Sarah N. Anderson, Peng Zhou, Maria Katherine Mejia Guerra, Zefu Lu, Christine H. O'Connor, Peter A. Crisp, Candice N. Hirsch, Robert J. Schmitz, Nathan M. Springer

Research output: Contribution to journalArticlepeer-review

Abstract

Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.

Original languageEnglish (US)
Article numberiyaa003
JournalGenetics
Volume217
Issue number1
DOIs
StatePublished - Jan 2021

Bibliographical note

Funding Information:
This work was funded by NSF IOS-1934384 to N.M.S. and C.N.H, NSF IOS-1856627 and NSF IOS-1844427 to R.J.S., and NSF IOS-1546727 to C.N.H. J.M.N. is supported by a Hatch grant from the Minnesota Agricultural Experiment Station (MIN 71-068). R.J.S. is a Pew Scholar in the Biomedical Sciences, supported by The Pew Charitable Trusts. A.P.M is supported by NSF PRFB IOS-1905869.

Funding Information:
This work was funded by NSF IOS-1934384 to N.M.S. and C.N.H, NSF IOS-1856627 and NSF IOS-1844427 to R.J.S., and NSF IOS- 1546727 to C.N.H. J.M.N. is supported by a Hatch grant from the Minnesota Agricultural Experiment Station (MIN 71-068). R.J.S. is a Pew Scholar in the Biomedical Sciences, supported by The Pew Charitable Trusts. A.P.M is supported by NSF PRFB IOS-1905869.

Publisher Copyright:
© The Author(s) 2020.

Keywords

  • ATAC-seq
  • Cis-regulatory regions
  • DNA methylation
  • Transposable elements
  • Zea mays

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